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configure.ac
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configure.ac
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# Process this file with autoconf to produce the HMMER configure script.
#
# Note that this is synchronized with Easel's configure script,
# so that HMMER configures Easel in addition to itself; this saves
# having to do a separate ./configure in Easel. That is,
# everything that appears in Easel's configure script must also
# appear here.
#
# reminders to save re-reading autoconf manual for the n'th time:
# output variables:
# - are defined here as normal shell variables, e.g. FOO="my string"
# - are made into output variables by calling AC_SUBST(FOO)
# - any occurrence of @FOO@ in an output file is then substituted
# I think this only happens in files we assign w/ AC_CONFIG_FILES;
# that's the Makefile.in's.
#
# C preprocessor symbols:
# - are defined here by calling AC_DEFINE(FOO) or AC_DEFINE(FOO, [42])
# - then #undef FOO in easel.h.in becomes #define FOO, #define FOO 42
# I think this only happens in header files that we assign
# w/ AC_CONFIG_HEADERS -- which means, easel.h.in
#
# SRE, Mon Oct 5 14:55:45 1998
# SVN $Id: configure.ac 3630 2011-08-03 14:09:27Z eddys $
# xref autoconf macro archive: //www.gnu.org/software/ac-archive/
#
# GNU recommends the following order:
# 1. autoconf requirements
# 2. AC_INIT
# 3. info on the package
# 4. checks for programs
# 5. checks for libraries
# 6. checks for header files
# 7. checks for types
# 8. checks for structures
# 9. checks for compiler characteristics
# 10. checks for library functions
# 11. checks for system services
# 12. AC_CONFIG_FILES
# 13. AC_OUTPUT
################################################################
# 1. autoconf requirements
################################################################
AC_PREREQ(2.63)
################################################################
# 2. AC_INIT
################################################################
AC_INIT(PKNOTS, 1.1, [email protected])
AC_MSG_NOTICE([Configuring PKNOTS for your system.])
# remember if the user is overriding CFLAGS
if test x"$CFLAGS" = x; then
sre_cflags_env_set=no
fi
################################################################
# 3. Info on the package
################################################################
#
# The four AC_INIT args above set the following output variables and preprocessor
# symbols:
# PACKAGE_NAME <package> e.g. "Easel"
# PACKAGE_VERSION <version> e.g. "0.2"
# PACKAGE_BUGREPORT <bug-report> e.g. "[email protected]"
# PACKAGE_TARNAME <tarname> e.g. "easel"
# From them, AC_INIT automatically derives one more:
# PACKAGE_STRING <package> <version>, e.g. "Easel 0.2"
# Then we define some of our own:
# EASEL_DATE release date: e.g. "February 2005"
# EASEL_COPYRIGHT one-line copyright string
# EASEL_LICENSE one-line license string
# EASEL_LICENSETAG which license to bundle from Licenses/ subdirectory.
# EASEL_URL URL home for Easel.
#
# Because Easel is designed to be a library and must coexist with
# packages that include it as a subdirectory (HMMER, Infernal...),
# we don't want to use AC_INIT's PACKAGE_ variables as preprocessor
# symbols to put version info into executables; we'll get name clashes,
# plus we might want to have both Easel version info and main package
# version info. So, we use the PACKAGE_ stuff to make a
# new preprocessor symbol of our own:
# EASEL_VERSION e.g. "1.9a"
#
PKNOTS_DATE="January 2018"
PKNOTS_COPYRIGHT="Copyright (C) 2010-2018 Howard Hughes Medical Institute."
PKNOTS_LICENSE="Freely distributed under the GNU General Public License (GPLv3)."
PKNOTS_VERSION="v1.1"
PKNOTS_URL="http://eddylab.org/"
PKNOTS_ESLDIR="lib/easel"
PKNOTS_HOME="`pwd`" #magic to get full path to current directory
AC_PREFIX_DEFAULT("`pwd`") #changes the prefix default from /usr/bin to PKNOTS_HOME
if test "$prefix" = NONE ; then
PKNOTS_BIN="`pwd`/bin"
else
PKNOTS_BIN=${prefix}/bin
fi
# Output variables (AC_OUTPUT replaces @var@ in input files, such as Makefiles)
AC_SUBST(PKNOTS_DATE)
AC_SUBST(PKNOTS_COPYRIGHT)
AC_SUBST(PKNOTS_LICENSE)
AC_SUBST(PKNOTS_VERSION)
AC_SUBST(PKNOTS_URL)
AC_SUBST(PKNOTS_ESLDIR)
# Preprocessor symbols (replace #undefs in pknots_config.h)
AC_DEFINE_UNQUOTED(PKNOTS_DATE, "$PKNOTS_DATE")
AC_DEFINE_UNQUOTED(PKNOTS_COPYRIGHT, "$PKNOTS_COPYRIGHT")
AC_DEFINE_UNQUOTED(PKNOTS_LICENSE, "$PKNOTS_LICENSE")
AC_DEFINE_UNQUOTED(PKNOTS_VERSION, "$PKNOTS_VERSION")
AC_DEFINE_UNQUOTED(PKNOTS_URL, "$PKNOTS_URL")
# Figure out what host we're compiling on.
# Three GNU scripts must be included in the distro:
# install.sh, config.guess, config.sub
# This sets four shell variables:
# host example: i686-pc-linux-gnu
# host_cpu example: i686
# host_vendor example: pc
# host_os example: linux-gnu
AC_CANONICAL_HOST
# Check if we're a binary distribution.
# Trigger is existence of binaries/, nonexistence of src/.
#
# For binary distro, we do minimal configuration, setting version information
# and installation path names, making ./configure independent of having a working
# C compiler.
#
# Implements a sneaky if statement that wraps most of the configure.ac M4 code.
#
#if ((! test -d binaries) && test -d src); then
AC_MSG_NOTICE([Full PKNOTS source distribution])
################################################################
# 4. Process ./configure command line options
################################################################
# --enable-debugging - set basic debugging (level 0)
# --enable-debugging=x - set debugging level to <x> (1-3)
#
# At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc).
# Sets p7_DEBUGGING preprocessor symbol, which compiles in debugging support.
# Also sets eslDEBUGLEVEL level, 0-3.
#
AC_ARG_ENABLE(debugging,
[AS_HELP_STRING([--enable-debugging],[include debugging code])
AS_HELP_STRING([--enable-debugging=x],[also set diagnostics verbosity level to <x> (1-3)])],
enable_debugging=$enableval, enable_debugging=no)
case $enable_debugging in
yes) AC_DEFINE(eslDEBUGLEVEL, 0);;
1) AC_DEFINE(eslDEBUGLEVEL, 1);;
2) AC_DEFINE(eslDEBUGLEVEL, 2);;
3) AC_DEFINE(eslDEBUGLEVEL, 3);;
no) AC_DEFINE(eslDEBUGLEVEL, 0);;
*) AC_MSG_ERROR([Unknown argument to --enable-debugging: $enable_debugging]);;
esac
# --enable-gcov - compile for code coverage testing
#
# Replaces CC with "gcc" and CFLAGS with "-g -Wall -fprofile-arcs -ftest-coverage".
# Running programs (notably the test suite) will then generate .gcda files,
# which the gcov tool can read.
#
AC_ARG_ENABLE(gcov,[AS_HELP_STRING([--enable-gcov],[compile for code coverage testing])], ok=$enableval, ok=no)
if test "$ok" = "yes"; then
AC_MSG_NOTICE([Compiling with gcov instrumentation.])
CC="gcc"
CFLAGS="-g -Wall -fprofile-arcs -ftest-coverage"
sre_cflags_env_set=yes
fi
# --enable-gprof - compile for gcc code profiling
#
# Replaces CC with "gcc" and CFLAGS with "-O -g -pg"
# Running programs generates a profile data file "gmon.out".
#
AC_ARG_ENABLE(gprof,[AS_HELP_STRING([--enable-gprof],[compile for gcc code profiing])], ok=$enableval, ok=no)
if test "$ok" = "yes"; then
AC_MSG_NOTICE([Compiling with gprof instrumentation.])
CC="gcc"
CFLAGS="-O -g -pg"
sre_cflags_env_set=yes
fi
# --enable-sse Enable the SSE implementation.
# --enable-vmx Enable the Altivec/VMX implementation.
# --enable-dummy Enable the portable implementation.
#
# These set $impl_choice to one of sse, vmx, dummy, or none.
#
AC_ARG_ENABLE(sse,[AS_HELP_STRING([--enable-sse],[enable SSE implementation])], enable_sse=$enableval, enable_sse=check)
AC_ARG_ENABLE(vmx,[AS_HELP_STRING([--enable-vmx],[enable Altivec/VMX implementation])], enable_vmx=$enableval, enable_vmx=check)
AC_ARG_ENABLE(dummy,[AS_HELP_STRING([--enable-dummy],[enable portable implementation])], enable_dummy=$enableval, enable_dummy=check)
if test "$enable_sse" = "yes"; then
if test "$enable_vmx" = "yes" || test "$enable_dummy" = "yes"; then
AC_MSG_ERROR([Select only one implementation of sse, vmx, or dummy])
fi
impl_choice=sse
elif test "$enable_vmx" = "yes"; then
if test "$enable_sse" = "yes" || test "$enable_dummy" = "yes"; then
AC_MSG_ERROR([Select only one implementation of sse, vmx, or dummy])
fi
impl_choice=vmx
elif test "$enable_dummy" = "yes"; then
if test "$enable_sse" = "yes" || test "$enable_vmx" = "yes"; then
AC_MSG_ERROR([Select only one implementation of sse, vmx, or dummy])
fi
impl_choice=dummy
else
impl_choice=none
fi
# --enable-mpi Enable MPI parallelization
AC_ARG_ENABLE(mpi,[AS_HELP_STRING([--enable-mpi],[enable MPI parallelization])], enable_mpi=$enableval, enable_mpi=no)
# --enable-xlc-arch Set the code generation for a particular architecture
#
# The xlc compiler on AIX seems to need the -qarch flag to be set for a processor
# that is VMX enabled. Otherwise a warning is issued that states the -qenablevmx
# and -qaltivec flags are ignored.
AX_COMPILER_VENDOR
if test "${ax_cv_c_compiler_vendor}" = "ibm"; then
AC_ARG_WITH(xlc-arch,
[AC_HELP_STRING([--with-xlc-arch=<arch>], [specify architecture <arch> for xlc -qarch])],
XLC_ARCH=$withval,
XLC_ARCH=no)
fi
# --enable-threads Enable POSIX multithreading
#
# Uses ACX_PTHREAD macro from the GNU macro archive.
# Back to my code to finish enabling pthreads...
# Define these preprocessor variables:
# HMMER_THREADS
# HAVE_PTHREAD_SETCONCURRENCY
# HAVE_PTHREAD_ATTR_SETSCOPE
#
AC_ARG_ENABLE([threads],
[AS_HELP_STRING([--enable-threads],
[enable POSIX multithreading support (default is check)])],
[],
[enable_threads=check])
case $enable_threads in
yes) check_threads=yes
;;
no) check_threads=no
;;
check) check_threads=yes
;;
*) check_threads=no
AC_MSG_NOTICE([Ignoring unknown argument to --enable-threads: $enable_threads])
;;
esac
AS_IF([test "x$check_threads" != xno],
[ACX_PTHREAD([AC_DEFINE(HMMER_THREADS)
AC_DEFINE(HAVE_PTHREAD)
AC_SUBST(PTHREAD_LIBS)
AC_SUBST(PTHREAD_CFLAGS)],
[if test "x$enable_threads" != xcheck; then
AC_MSG_FAILURE([POSIX multithreading failed])
fi])])
#AC_ARG_ENABLE(threads,
#[ --enable-threads enable POSIX multithreading support],
#[case $enable_threads in
# yes) AC_MSG_NOTICE([enabled POSIX multithreading support])
# AC_CHECK_FUNCS(pthread_setconcurrency)
# AC_CHECK_FUNCS(pthread_attr_setscope)
# ACX_PTHREAD(AC_DEFINE(HMMER_THREADS))
# ;;
# no) AC_MSG_NOTICE([POSIX multithreading support disabled])
# ;;
# *) echo "Ignoring unknown argument to --disable-threads: $enable_threads"
# ;;
#esac])
# --with-gsl - enable hooks into the GSL (GNU Scientific Library)
#
# The (action-if-given) is blank: using --with-gsl sets $with_gsl to 'yes',
# and --without-gsl sets $with_gsl to 'no'. If neither is given,
# $with_gsl is set to 'check', and we'll try to use GSL anyway if we
# can find it.
#
# We interpret the $with_gsl setting later, in the "checks for libraries" section.
AC_ARG_WITH([gsl],
[AS_HELP_STRING([--with-gsl],
[use the GSL, GNU Scientific Library (default is no)])],
[if test "x$withval" != xno ; then
AC_MSG_NOTICE([Enabling hooks into the GNU Scientific Library (GSL)])
fi
],
[with_gsl=no])
################################################################
# Select the vector implementation we'll use
# (if user didn't already configure one)
#
if test "$impl_choice" = "none"; then
case $host in
ia64-*-*) impl_choice=sse;;
i?86-*-*) impl_choice=sse;;
x86*-*-*) impl_choice=sse;;
powerpc*-*-*) impl_choice=vmx;;
*) impl_choice=dummy;;
esac
fi
if test "$impl_choice" = "dummy"; then
AC_MSG_WARN([It appears your platform will not fully support H3.])
AC_MSG_WARN([We'll use the 'dummy' implementation, a slow reference implementation.])
fi
if test "$impl_choice" = "sse" && test "$enable_sse" = "no"; then
AC_MSG_WARN([You disabled the SSE implementation: I'll use the dummy impl instead.])
impl_choice=dummy
fi
if test "$impl_choice" = "vmx" && test "$enable_vmx" = "no"; then
AC_MSG_WARN([You disabled the VMX implementation: I'll use the dummy impl instead.])
impl_choice=vmx
fi
if test "$impl_choice" = "dummy" && test "$enable_dummy" = "no"; then
AC_MSG_ERROR([No vector impl configured; and you disabled the dummy implementation.])
fi
################################################################
# 5. Checks for programs, including ${CC} and its ${CFLAGS}
################################################################
AC_PROG_CC
AC_PROG_INSTALL
# MPI : set @CC@ to mpicc, sets @MPILIBS@, defines HAVE_MPI.
if test "$enable_mpi" = "yes"; then
ACX_MPI([AC_DEFINE(HAVE_MPI)
AC_SUBST([MPI_UTESTS], ["mpi_utest"])
AC_SUBST([MPI_BENCHMARKS], ["mpi_benchmark"])],
AC_MSG_ERROR([MPI library not found for --enable-mpi]))
CC=$MPICC
fi
AC_PROG_CPP
AX_COMPILER_VENDOR
# AC_PROG_CC_STDC wants to append -c99 to icc; icc doesn't like this.
if test "$ax_cv_c_compiler_vendor" != "intel"; then
AC_PROG_CC_STDC
fi
AC_PROG_RANLIB
AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
CHECK_GNU_MAKE
# Select our optimization level in CFLAGS.
if test "$enable_debugging" != "no"; then
AC_DEFINE(p7_DEBUGGING, 1)
if test "$GCC" = "yes" && test "$sre_cflags_env_set" = "no"; then
CFLAGS="-g -Wall"
fi
else
sre_save_ac_test_cflags="$ac_test_CFLAGS"
if test "$sre_cflags_env_set" = "no"; then
ac_test_CFLAGS=""
fi
AX_CC_MAXOPT
ac_test_CFLAGS="$sre_save_ac_test_cflags"
# That was a workaround. AX_CC_MAXOPT apparently thinks that
# $ac_test_CFLAGS only gets set if ${CFLAGS} was set by the
# user (in the environment), but that's not so; it gets set
# by AC_PROG_CC. Instead of rewriting AX_CC_MAXOPT, we fool
# it.
fi
# Figure out how to generate PIC code for shared libraries
# This sets @PIC_FLAGS@ output variable for Easel.
ESL_PIC_FLAGS
# If we're using SSE, figure out our @SIMD_CFLAGS@
if test "$impl_choice" = "sse" && test "x$SIMD_CFLAGS" = x; then
case $ax_cv_c_compiler_vendor in
gnu) AX_CHECK_COMPILER_FLAGS(-msse2,[SIMD_CFLAGS="-msse2"],[impl_choice=dummy]);;
intel) ;;
*) ;;
esac
fi
if test "$enable_sse" = "yes" && test "$impl_choice" = dummy; then
AC_MSG_ERROR([SSE instructions are apparently not available; --enable-sse failed])
fi
# If we're using VMX/Altivec, figure out our @SIMD_CFLAGS@
if test "$impl_choice" = "vmx"; then
if test "x$SIMD_CFLAGS" = x; then
if test "$GCC" = "yes"; then
# -DFAKE__VEC__ is a workaround because gcc-3.3 does not
# #define __VEC__ with -maltivec.
AX_CHECK_COMPILER_FLAGS(-faltivec, [SIMD_CFLAGS="-faltivec"],
[AX_CHECK_COMPILER_FLAGS(-maltivec -mabi=altivec,
[SIMD_CFLAGS="-maltivec -mabi=altivec"],
# [SIMD_CFLAGS="-maltivec -mabi=altivec -DFAKE__VEC__"],
[AX_CHECK_COMPILER_FLAGS(-fvec, [SIMD_CFLAGS="-fvec"],
[AC_MSG_ERROR([Need a version of gcc with -maltivec])])])])
elif test "${ax_cv_c_compiler_vendor}" = "ibm"; then
SIMD_CFLAGS=""
# if debugging is enabled and the xlc_arch flag is set, we need to
# set the qarch flag here. if debugging is NOT enabled, the arch
# flag is set in AX_CC_MAXOPT.
if test "x$XLC_ARCH" != x; then
if test "x$enable_debugging" = xyes; then
AX_CHECK_COMPILER_FLAGS(-qarch=$XLC_ARCH, [SIMD_CFLAGS="-qarch=$XLC_ARCH"],[])
fi
fi
AX_CHECK_COMPILER_FLAGS(-qenablevmx, [SIMD_CFLAGS="$SIMD_CFLAGS -qenablevmx"],[])
AX_CHECK_COMPILER_FLAGS(-qaltivec, [SIMD_CFLAGS="$SIMD_CFLAGS -qaltivec"],[])
else
AX_CHECK_COMPILER_FLAGS(-faltivec, [SIMD_CFLAGS="-faltivec"],[])
fi
fi
fi
# Figure out how to generate PIC code for shared libraries
# This sets @PIC_FLAGS@ output variable for Easel.
ESL_PIC_FLAGS
# If we're using SSE, figure out our @SIMD_CFLAGS@
if test "$impl_choice" = "sse" && test "x$SIMD_CFLAGS" = x; then
case $ax_cv_c_compiler_vendor in
gnu) AX_CHECK_COMPILER_FLAGS(-msse2,[SIMD_CFLAGS="-msse2"],[impl_choice=dummy]);;
intel) ;;
*) ;;
esac
fi
if test "$enable_sse" = "yes" && test "$impl_choice" = dummy; then
AC_MSG_ERROR([SSE instructions are apparently not available; --enable-sse failed])
fi
# If we're using VMX/Altivec, figure out our @SIMD_CFLAGS@
if test "$impl_choice" = "vmx"; then
if test "x$SIMD_CFLAGS" = x; then
if test "$GCC" = "yes"; then
# -DFAKE__VEC__ is a workaround because gcc-3.3 does not
# #define __VEC__ with -maltivec.
AX_CHECK_COMPILER_FLAGS(-faltivec, [SIMD_CFLAGS="-faltivec"],
[AX_CHECK_COMPILER_FLAGS(-maltivec -mabi=altivec,
[SIMD_CFLAGS="-maltivec -mabi=altivec"],
# [SIMD_CFLAGS="-maltivec -mabi=altivec -DFAKE__VEC__"],
[AX_CHECK_COMPILER_FLAGS(-fvec, [SIMD_CFLAGS="-fvec"],
[AC_MSG_ERROR([Need a version of gcc with -maltivec])])])])
elif test "${ax_cv_c_compiler_vendor}" = "ibm"; then
SIMD_CFLAGS=""
# if debugging is enabled and the xlc_arch flag is set, we need to
# set the qarch flag here. if debugging is NOT enabled, the arch
# flag is set in AX_CC_MAXOPT.
if test "x$XLC_ARCH" != x; then
if test "x$enable_debugging" = xyes; then
AX_CHECK_COMPILER_FLAGS(-qarch=$XLC_ARCH, [SIMD_CFLAGS="-qarch=$XLC_ARCH"],[])
fi
fi
AX_CHECK_COMPILER_FLAGS(-qenablevmx, [SIMD_CFLAGS="$SIMD_CFLAGS -qenablevmx"],[])
AX_CHECK_COMPILER_FLAGS(-qaltivec, [SIMD_CFLAGS="$SIMD_CFLAGS -qaltivec"],[])
else
AX_CHECK_COMPILER_FLAGS(-faltivec, [SIMD_CFLAGS="-faltivec"],[])
fi
fi
fi
# check if the SSE2 implementation support cast functions
if test "$impl_choice" = "sse"; then
AC_MSG_CHECKING([compiler support for sse2 cast functions])
ssecast=no
sre_save_cflags="$CFLAGS"
CFLAGS="$CFLAGS $SIMD_CFLAGS"
AC_LANG(C)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <emmintrin.h>]],
[[__m128 a;
__m128i b;
b = _mm_castps_si128(a);
a = _mm_castsi128_ps(b);]])],
[AC_DEFINE([HAVE_SSE2_CAST])
ssecast=yes])
AC_MSG_RESULT([$ssecast])
CFLAGS="$sre_save_cflags"
fi
# Verify that we can actually build the chosen implementation; else
# default to dummy.
# (For example, Athlon reports as i686-*, so will get assigned to
# sse impl, but does not support SSE2 instructions.)
# The test here is cribbed from the Apache configure.ac file.
#
if test "$impl_choice" = "sse"; then
AC_MSG_CHECKING([whether SSE2 is supported])
sre_save_cflags="$CFLAGS"
CFLAGS="$CFLAGS $SIMD_CFLAGS"
AC_COMPILE_IFELSE( [AC_LANG_PROGRAM([[#include <emmintrin.h>]],
[[__m128i* one=(__m128i*)_mm_malloc(4, 16);
__m128i* two=(__m128i*)_mm_malloc(4, 16);
__m128i xmm1 = _mm_load_si128(one);
__m128i xmm2 = _mm_load_si128(two);
__m128i xmm3 = _mm_or_si128(xmm1, xmm2);
_mm_store_si128(one, xmm3);
_mm_free(one);
_mm_free(two);
]])],
[ AC_MSG_RESULT([yes])],
[ AC_MSG_RESULT([no; reverting to dummy implementation])
impl_choice=dummy
]
)
CFLAGS="$sre_save_cflags"
fi
if test "$impl_choice" = "vmx"; then
AC_MSG_CHECKING([whether Altivec/VMX is supported])
sre_save_cflags="$CFLAGS"
CFLAGS="$CFLAGS $SIMD_CFLAGS"
AC_COMPILE_IFELSE( [AC_LANG_PROGRAM([[#include <altivec.h>]],
[[vector unsigned char zerov;
vector unsigned char onev;
zerov = vec_splat_u8(0);
onev = vec_splat_u8(1);
onev = vec_adds(onev, zerov);
]])],
[ AC_MSG_RESULT([yes])],
[ AC_MSG_RESULT([no; reverting to dummy implementation])
impl_choice=dummy
if test "${ax_cv_c_compiler_vendor}" = "ibm"; then
echo "******************************************************"
echo "* You seem to have the IBM C compiler. If your *"
echo "* processor supports vector instructions it is *"
echo "* possible specifying an architecture would enable *"
echo "* vector support, i.e. *"
echo "* *"
echo "* --with-xlc-arch=XXX *"
echo "* *"
echo "* where XXX is pwr6, auto or whatever kind of CPU *"
echo "* you have. *"
echo "******************************************************"
fi
]
)
CFLAGS="$sre_save_cflags"
fi
# For x86 processors check if the flush to zero macro is available
# in order to avoid the performance penalty dealing with sub-normal
# values in the floating point calculations.
if test "$impl_choice" = "sse"; then
AC_MSG_CHECKING([whether _MM_SET_FLUSH_ZERO_MODE is supported])
sre_save_cflags="$CFLAGS"
CFLAGS="$CFLAGS $SIMD_CFLAGS"
AC_COMPILE_IFELSE( [AC_LANG_PROGRAM([[#include <xmmintrin.h>]],
[[_MM_SET_FLUSH_ZERO_MODE (_MM_FLUSH_ZERO_ON);
]])],
[ AC_MSG_RESULT([yes])
AC_DEFINE([HAVE_FLUSH_ZERO_MODE])],
[ AC_MSG_RESULT([no])]
)
CFLAGS="$sre_save_cflags"
fi
# Define HAVE_GZIP if gzip is in $PATH (or if HAVE_GZIP is already set)
AC_PATH_PROG(HAVE_GZIP, "gzip", "no")
if test "${HAVE_GZIP}" = "no"; then
AC_MSG_WARN([gzip not found])
else
AC_DEFINE(HAVE_GZIP)
fi
################################################################
# 6. Checks for libraries
#################################################################
LIBGSL=
AS_IF([test "x$with_gsl" != xno],
[AC_CHECK_LIB([gsl], [gsl_expm1],
[AC_SUBST([LIBGSL], ["-lgsl -lgslcblas"])
AC_DEFINE([HAVE_LIBGSL], [1], [Define if you have libgsl])
],
[if test "x$with_gsl" != xcheck; then
AC_MSG_FAILURE(
[--with-gsl was given, but GSL library was not found])
fi
],
[-lgslcblas]
)])
################################################################
# 7. Checks for headers
################################################################
AC_CHECK_HEADERS([sys/types.h sys/sysctl.h unistd.h stdint.h inttypes.h endian.h])
# altivec.h requires the simd cflags
# For reasons I don't understand, this needs to come after any other CHECK_HEADERS().
if test "$impl_choice" = "vmx"; then
sre_save_CFLAGS="$CFLAGS"
sre_save_CPPFLAGS="$CPPFLAGS"
CFLAGS="$CFLAGS $SIMD_CFLAGS"
CPPFLAGS="$CPPFLAGS $SIMD_CFLAGS"
AC_CHECK_HEADERS([altivec.h])
CFLAGS="$sre_save_CFLAGS"
CPPFLAGS="$sre_save_CPPFLAGS"
fi
################################################################
# 8. Checks for types
################################################################
# - Define WORDS_BIGENDIAN on bigendian platforms.
# - Make sure we have C99 exact-size integer types;
# ssi uses 16, 32, and 64-bit ints, and we
# use 8-bit unsigned chars for digitized sequence.
# - Make sure we have off_t.
#
AC_C_BIGENDIAN
AC_TYPE_UINT8_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_TYPE_OFF_T
################################################################
# 9. Checks for structures - currently none
#################################################################
################################################################
# 10. Checks for compiler characteristics
#################################################################
################################################################
# 11. Checks for library functions: define HAVE_FOO
################################################################
AC_CHECK_FUNCS(mkstemp)
AC_CHECK_FUNCS(popen)
AC_CHECK_FUNCS(strcasecmp)
AC_CHECK_FUNCS(times)
AC_CHECK_FUNCS(getpid)
AC_CHECK_FUNCS(sysctl)
AC_CHECK_FUNCS(sysconf)
AC_CHECK_FUNCS(getcwd)
AC_CHECK_FUNCS(stat)
AC_CHECK_FUNCS(fstat)
AC_CHECK_FUNCS(ntohs, , AC_CHECK_LIB(socket, ntohs))
AC_CHECK_FUNCS(ntohl, , AC_CHECK_LIB(socket, ntohl))
AC_CHECK_FUNCS(htons, , AC_CHECK_LIB(socket, htons))
AC_CHECK_FUNCS(htonl, , AC_CHECK_LIB(socket, htonl))
AC_FUNC_FSEEKO
#################################################################
# 12. System services
#################################################################
AC_SYS_LARGEFILE
#################################################################
# 13. Write out esl_config.h header and the Makefiles
#################################################################
AC_CONFIG_HEADERS([
src/pknots_config.h
])
AC_CONFIG_SUBDIRS(lib/easel)
AC_CONFIG_FILES([
Makefile
src/Makefile
lib/easel/Makefile
])
#################################################################
# 14. et voila!
#################################################################
AC_OUTPUT
echo "
PKNOTS configuration:
compiler: ${CC} ${CFLAGS} ${SIMD_CFLAGS} ${PTHREAD_CFLAGS} ${PIC_FLAGS}
host: $host
linker: ${LDFLAGS}
libraries: ${LIBS} $
"